Phylogeny and evolution of Adephaga and Neuropterida (Insecta: Holometabola) as inferred from analyses of next-generation sequencing data

Abstract

Knowing the evolutionary relationships of species is fundamental for comparative studies in biology as well as for biodiversity conservation. The main topic of this thesis is the investigation of phylogenetic relationships of two groups of holometabolous insects: Adephaga and Neuropterida. The phylogenetic analyses performed here were based on extensive genomic data that were obtained using two genome-reduction approaches: 1) transcriptomics and 2) hybrid enrichment of protein-coding exons. Several methods were applied to alleviate potential errors in the phylogenetic inferences such as: a) different data-subsampling strategies and b) application of methods and models that take into account different types of heterogeneity in the data. Evaluation of inferred evolutionary hypotheses was performed using a combination of methods such as: 1) different quartet-based measures of phylogenetic incongruence applied together with commonly used branch support measures, 2) congruency tests with morphology-based phylogenies, 3) comparisons of results from analyses of different data types (i.e., amino acids and nucleotides) and 4) comparison of results between best-fitting and less-fitting models of molecular evolution. This combination of methods and data was applied for the first time here to infer the phylogeny of Adephaga and Neuropterida. In general, these integrative phylogenomic approaches for species-tree inference and for evaluating inferred evolutionary hypotheses result in a better understanding of the phylogeny Adephaga and Neuropterida but they also help to identify unresolved or difficult phylogenetic questions in the backbone phylogeny of these groups and potentially also in other groups of species. Additionally, the presented approaches for critically evaluating results of phylogenomic analyses constitute a valuable resource for future studies focusing on the reconciliation of molecular and morphological phylogenies.<br /> In chapter 1, I provide a general introduction to the field of molecular systematics and phylogenomics and a brief introduction to the phylogeny of Adephaga and Neuropterida. In chapter 2, I assemble a large transcriptomic dataset to infer the phylogeny and divergence times of Neuropterida and I evaluate the inferred results using different measures of phylogenomic incongruence. In chapter 3, I focus on the phylogenetic relationships within the adephagan superfamily Dytiscoidea, using transcriptomes, and I apply data-subsampling strategies in order to reduce deviation of data from the model assumptions. I also evaluate the phylogenetic results using concatenation-based and gene tree-based measures of phylogenomic incongruence. In chapter 4, I infer a new set of DNA-hybridization baits suitable for capturing hundreds of protein-coding exons for phylogenetic investigations in the beetle suborder Adephaga. New hybrid-enrichment data for all major lineages of the suborder were then generated and were combined with transcriptomes to produce the most species-rich phylogenomic taxon sampling for Adephaga presented to date. I use this dataset to infer the phylogeny of Adephaga and I perform evaluation-focused exploratory analyses with different evolutionary models and with quartet-based measures of phylogenetic incongruence. Lastly in chapter 5, I discuss the most important results of this thesis in the historical context of knowledge on the phylogeny of these groups and I provide useful directions and advice for overcoming the limits of phylogenomic data and methods in future molecular systematic studies.